feat(coding-agent): add packages array with filtering support

- Add PackageSource type for npm/git sources with optional filtering
- Migrate npm:/git: sources from extensions to packages array
- Add getPackages(), setPackages(), setProjectPackages() methods
- Update package-manager to resolve from packages array
- Support selective loading: extensions, skills, prompts, themes per package
- Update pi list to show packages
- Add migration tests for settings

closes #645

packages/coding-agent/CHANGELOG.md

@@ -5,6 +5,7 @@
 ### Breaking Changes
 
 - Header values in `models.json` now resolve environment variables (if a header value matches an env var name, the env var value is used). This may change behavior if a literal header value accidentally matches an env var name. ([#909](https://github.com/badlogic/pi-mono/issues/909))
+- External packages (npm/git) are now configured via `packages` array in settings.json instead of `extensions`. Existing npm:/git: entries in `extensions` are auto-migrated. ([#645](https://github.com/badlogic/pi-mono/issues/645))
 - Resource loading now uses `ResourceLoader` only and settings.json uses arrays for extensions, skills, prompts, and themes ([#645](https://github.com/badlogic/pi-mono/issues/645))
 - Removed `discoverAuthStorage` and `discoverModels` from the SDK. `AuthStorage` and `ModelRegistry` now default to `~/.pi/agent` paths unless you pass an `agentDir` ([#645](https://github.com/badlogic/pi-mono/issues/645))
 
@@ -14,6 +15,7 @@
 - Header values in `models.json` now support environment variables and shell commands, matching `apiKey` resolution ([#909](https://github.com/badlogic/pi-mono/issues/909))
 - `markdown.codeBlockIndent` setting to customize code block indentation in rendered output
 - Extension package management with `pi install`, `pi remove`, `pi update`, and `pi list` commands ([#645](https://github.com/badlogic/pi-mono/issues/645))
+- Package filtering: selectively load resources from packages using object form in `packages` array ([#645](https://github.com/badlogic/pi-mono/issues/645))
 - `/reload` command to reload extensions, skills, prompts, and themes ([#645](https://github.com/badlogic/pi-mono/issues/645))
 - CLI flags for `--skill`, `--prompt-template`, `--theme`, `--no-prompt-templates`, and `--no-themes` ([#645](https://github.com/badlogic/pi-mono/issues/645))
 - Show provider alongside the model in the footer if multiple providers are available